B.1.617.2 is decreasing primarily because these sequences are being classified as other sublineages. Otherwise, the Delta AY sublineage frequencies are remaining very stable and there is currently *no evidence that any are more transmissible* in Connecticut. (3/6)
Here is my previous tweet + thread that explains what mutations are associated with the common Delta sublineages in Connecticut. (4/6)
The 7-day moving average case counts in Connecticut are also remaining stable despite modeled estimates of decreased infections. Delta is proving to be very hard to control. (5/6)
This week I'd like to thank the Yale Center for Outcome Research and Evaluation (CORE), Dave Ferguson + @wade_schulz, for working with us every week to provide samples for sequencing. It's hard work, and we really appreciate it! πͺ(6/6)
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Delta sub-lineage AY.12, with the Spike T791I mutation, has received some attention because its 60-80% in Israel, but its not currently increasing globally. Its been mostly hovering between 4-6% since mid-June.
Alpha is the first variant to hit the news, and concern over its emergence was the primary motivating factor for the construction of our state genomic surveillance system. Because of our rapid increase in sequencing, we've been able to detect other variants much earlier. (3/10)
Besides Delta, the other major story here is B.1.621. It's now firmly the second most frequent variant in CT (~8%), and has so far been able to maintain its ground against the expansion of Delta. Something that Alpha, Gamma, and everything else couldn't do. (3/9)
All of our B.1.621 + B.1.621.1 (important emerging SARS-CoV-2 variant) submissions are being rejected by GISIAD. This has some important implications that data producers + public health agencies should be aware of.
Technical π§΅(1/12)
We usually have a few sequences/week that get rejected for QC reasons (eg indel in a string of As or Ts). It takes a few days for these to be fixed and reposted. Sometimes longer depending on our bandwidth. These are usually a random distribution so not a problem if delayed(2/12)
This past week we had 40+ sequences get rejected, and almost all of them were B.1.621/B.1.621.1. @JosephFauver found that all of these sequences have a 4 nt deletion in ORF3A that results in a premature stop codon about ~50 nt upstream. GISAID sees these and kicks them back(3/12)